In my opinion, pertaining to your case of "empty links", does it affect SEO? The answer probably lies in the amount of it. Maybe there is no direct impact if there is maybe 1 or 2 or even 10 links. In summary, yes it does affect SEO in the sense of it is not able to pass the juice. Think about a nice or highly searched keyword in an article - [Some nice keywords] and this anchor text does not go anywhere. The link equity probably gets passed no where and probably limited to that page only. With regards to relevance, it will probably give search engines signals that this page is no longer relevant and therefore affecting the frequency of the crawl for that domain/subdomain/page. Indirectly and overtime, this will affect SERP for that domain.
As far as how many empty href wills start affecting SEO? It will be interesting to see this experiment. Any takers? I'll leave this to the SEO heavy weights or SEO nerds.
Correction: I agree to Andy's comment below.
